# Doctor of Philosophy in Interdisciplinary Studies: Specialization in Bioinformatics

**Major:**IS_PHDINFO

**Degree Awarded:**Ph.D.

**Unit:**IS

**Program Webpage:**http://bioinformatics.louisville.edu/

## Program Information

**Program Executive Committee Chair**

**General Information**

- Biomedical and Natural Sciences
- Computational Sciences
- Mathematics and Statistics

Students in the Bioinformatics Program specialize in one of the three focus application areas and graduate with cutting-edge expertise in this area and working knowledge in the other two focus application areas.

[i] “Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources.” National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html. Revised: March 29, 2004.

## Curriculum

**Graduate Studies -- Ph.D.**

To earn the Doctor of Philosophy in Interdisciplinary Studies: Concentration in Bioinformatics, a student is required to successfully complete the following:

Core coursework in the focus application areas

Required coursework in the student’s area of specialization

Elective courses in the student’s area of specialization

Qualifying examination

Dissertation

Presentation and defense of dissertation

Good standing requires that the student maintain a minimum 3.0 grade point average.Upon successful completion of the written and oral portions of the qualifying examination, the examination committee will recommend acceptance into Ph.D. candidacy. Successful completion of the dissertation and its presentation and defense is established by the approval of the student’s dissertation committee and the approval of the chair of the sponsoring department and the program chair.

**Programs of Study**

Course requirements for the Interdisciplinary Ph.D. Degree Program in Bioinformatics consist of 16 core credit hours (that will be conditional based upon focus area) and 21 credit hours derived from a combination of required courses from a chosen focus area and electives from each of the three focus areas. Students with an appropriate background in the biomedical and natural sciences may petition to substitute a course in either the Computational Sciences or Mathematics and Statistics focus for the core course BIOC 545 Biochemistry I, and a corresponding course in either the Computational Sciences or Mathematics and Statistics for MBIO 667 Graduate Cell Biology, thus maintaining 16 core credit hours. Following acceptance into a focus area, students will be required to complete three courses totaling at least nine hours from the declared focus area. At least four additional elective courses (12 credit hours) will be selected from available elective courses, with the provision that two elective courses must be selected in each of the other two focus areas. The Program of Study will be determined by the student and approved by both an advisor residing in a declared focus area department and the Executive Committee. The following tables list the required courses for the core as well as the required and elective courses in each of the focus areas. Students must accumulate at least nine credit hours of dissertation.

**Core Course Work**

Department | Course | Description | Credits |

BIOC | 545*† | Biochemistry I | 3 |

BIOC | 630* | Responsible Conduct of Research: Survival Skills and Research Ethics | 1 |

MBIO | 667* | Graduate Cell Biology | 3 |

PSYCH | 571/609^{#} | Computational Cognitive Science I | 3 |

CECS | 660* | Introduction to Bioinformatics | 3 |

PHBI | 750* | Statistical Methods for Bioinformatics | 3 |

*All courses are required. ^{†}CHEM 645 may be substituted. Students may take either the BIOC 545/BIOC547 or CHEM 645/647 sequence but are not allowed to take the sequence BIOC 545/CHEM647 or CHEM 645/BIOC547. ^{#}Cross-listed as CECS 590-02.

**Courses in Mathematics and Statistics **

Department | Course | Description | Credits |

MATH | 505 | Introduction to Partial Differential Equations | 3 |

MATH | 507 | Fourier Series | 3 |

MATH | 561# | Probability | 3 |

PHYS | 565 | Computational Physics | 3 |

MATH | 566 | Nonparametric Statistical Methods | 3 |

PHYS | 625 | Statistical Mechanics | 3 |

PHST | 630 | Applied Statistical Models | 3 |

MATH | 636 | Mathematical Modeling II | 3 |

MATH | 660 | Probability Theory | 3 |

PHST | 661# | Probability | 3 |

PHST | 662# | Mathematical Statistics | 3 |

MATH | 562/662# | Advanced Mathematical Statistics | 3 |

MATH | 665 | Advanced Linear Statistical Models | 3 |

MATH | 667* | Methods of Classification | 3 |

MATH | 670 | Introduction to Stochastic Calculus | 3 |

MATH | 681 | Combinatorics and Graph Theory I | 3 |

MATH | 682 | Combinatorics and Graph Theory II | 3 |

PHST | 682 | Multivariate Statistical Analysis | 3 |

PHST | 691 | Bayesian Inference and Decision | 3 |

PHST | 710 | Advanced Statistical Computing | 3 |

PHST | 711 | Advanced Statistical Computing II | 3 |

PHST | 725 | Design of Experiments | 3 |

PHBI | 751 | High-throughput Data Analysis | 3 |

PHBI | 752 | Statistical Genetics | 3 |

PHST | 762 | Advanced Statistical Inference | 3 |

PHST | 780 | Advanced Nonparametric Statistics | 3 |

PHST | 781 | Advanced Linear Models | 3 |

PHST | 782 | Generalized Linear Models | 3 |

#Credit only for one: MATH 561/PHST 661; MATH 562/PHST 662

**Courses in Biomedical and Natural Sciences **

Department | Course | Description | Credits |

BIOL | 542 | Gene Structure and Function | 3 |

BIOL | 569 | Evolution | 3 |

BIOC | 680 | Biomolecular Interactions | 3 |

BIOC | 611 | Biochemical and Molecular Methods | 4 |

ASNB | 614 | Molecular Neuroscience | 4 |

BIOC | 641 | Advanced Eukaryotic Genetics | 3 |

BIOC | 647# | Advanced Biochemistry II | 4 |

CHEM | 647 | Advanced Biochemistry II | 4 |

CHEM | 648 | Systems Biochemistry Principles and Practices | 3 |

CHEM | 652 | Practical Approaches to Metabolomics | 3 |

BIOC | 661 | Molecular Mechanisms of Toxicology | 3 |

BIOC | 668 | Molecular Biology | 3 |

BIOC | 670 | Protein Structure and Function | 4 |

CHEM | 684 | Biophysical Chemistry | 3 |

#Credit only for one: CHEM 645/BIOC 645, CHEM 647/BIOC 647. Students may take either the BIOC 545/BIOC547 or CHEM 645/647 sequence but are not allowed to take the sequence BIOC 545/CHEM647 or CHEM 645/BIOC547.

**Courses in Computational Sciences **

Department | Course | Description | Credits |

CECS | 535 | Introduction to Databases | 3 |

CECS | 546 | Knowledge Engineering and Expert Systems | 3 |

CECS | 619 | Design and Analysis of Computer Algorithms | 3 |

CECS | 622 | Simulation and Modeling of Discrete Engineering Systems | 3 |

CECS | 624 | Advanced Simulation | 3 |

CECS | 627 | Digital Image Processing | 3 |

CECS | 628 | Computer Graphics | 3 |

CECS | 629 | Distributed System Design | 3 |

CECS | 630 | Advanced Databases and Data Warehousing | 3 |

CECS | 632 | Data Mining | 3 |

CECS | 641 | Introduction to Medical Imaging | 3 |

CECS | 643 | Introduction to Biomedical Computing | 3 |

CECS | 645 | Advanced Artificial Intelligence | 3 |

CECS | 646 | Intelligent Systems | 3 |

## Departmental Faculty

### Participating Faculty for the Bioinformatics Program have primary appointments in various departments across the University, including:

**College of Arts and Sciences**: Departments of Biology, Chemistry, Mathematics, and Psychological and Brian Sciences**J.B. Speed School of Engineering**: Department of Computer Engineering and Computer Science**School of Medicine**: Departments of Anatomical Sciences and Neurobiology and Biochemistry and Molecular Biology**School of Public Health and Information Sciences**: Departments of Bioinformatics and Biostatistics, Environmental Health and Occupational Health Sciences, and Epidemiology and Population Health

**Faculty**

**Eric C. Rouchka**, Executive Committee Chair

*D.Sc., Washington University in St. Louis*

**Theodore S. Kalbfleisch**, Executive Committee Vice-Chair

*Ph.D., Boston University*

**Guy Brock**

*Ph.D., University of New Mexico*

**Nigel G.F. Cooper**

*Ph.D., University of Tennessee Health Sciences Center*

**Somnath Datta**

*Ph.D., Michigan State University*

**Susmita Datta**

*Ph.D., University of Georgia*

**Ryan Gill**

*Ph.D., The University of Texas at Dallas*

**Gary Hoyle**

*Ph.D., Duke University*

**Richard Kerber**

*Ph.D., Northwestern University*

**Seongho Kim**

*Ph.D., Korea Advanced Institute of Science and Technology*

**Jiaxu Li**

*Ph.D., Arizona State University*

**Hunter Moseley**

*Ph.D., University of Alabama at Birmingham*

**Rachel Neal**

*Ph.D., University of Missouri-Rolla*

**Liz O'Brien**

*Ph.D., Northwestern University*

**Ming Ouyang**

*Ph.D., Rutgers University*

**Michael Perlin**

*Ph.D., University of Chicago*

**Jeffrey C. Petruska**

*Ph.D., University of Florida*

**Patrick Shafto**

*Ph.D., Northeastern University*

**David Schultz**

*Ph.D., Pennsylvania State University*

**Xiang Zhang**

*Ph.D., Purdue University*